Wasn't there something in OMD to the effect that Peter's and MJ's memories of what had been, wouldn't be completely erased, and that a part of them still remembered? Fanatical as Quesada has indeed been about his hatred of Married!Spidey, it seems to me that he might've wanted to leave a way out. Or maybe that was the writer's idea, snuck under Quesada's radar.
I admit that's just conjecture, and I'm more than likely wrong. (A first for this thread, methinks...heh.)